Hallo guys,
Can someone please suggest to me how I can use the following input search parameters for my tblastn search(using standalone BLAST):
Searching parameters : maximum identity > 95%, length > 200 bp and Evalue < 10e-10 (borrowed idea from http://www.biomedcentral.com/1471-2164/12/76); topic;digital expression analysis.
I am well conversant with the normal input parameters such as
tblastn -db blastdb/nippest -query mydata.fasta -evalue 10e-10 > out.nipest -outfmt 7.
Following the attached paper I wish to add maximum identity>95% and length >200 but I can't figure out...
Thanks.
For the question "But how do you use adobe illustrator to display various gene position in a chromosome?" see: Drawing Chromosome Ideograms With Data
inkscape.org is a good alternative to illustrator.
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Pierre Lindenbaum
I want something which can display relationship of varius genes. For example a line connecting duplicated genes (duplicate1 to duplicate 2) as outlined in this papers;
This post won't give me what I want. I have not used inkscape before let me have a look at it
Thanks Pierre and Devon
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then tell us what's your input and what you want to achieve.
P.
Figure 2b looks like a job for Circos, and figure 1 from the other paper could just be done with Adobe Illustrator (or equivalent).
Yes figure 2 is circos work, that's what I have been trying to use but got above error messages.. I have posted my question to circos group but I haven't found a solution. But how do you use adobe illustrator to display various gene position in a chromosome?
The position information in graphics like this doesn't need to be exact (you're not measuring pixels here), so you can just put something together by hand. If you have a lot of positions to plot then this is a no-go, but with just a handful it's likely to be faster than learning a bunch of new packages.
i got alot of positions to plot...roughly 500 gene duplication positions though some genes duplicated to many genes hence they will share postions.as in gene A gave rise to geneB,geneC and geneD.
Then you'll need to find or code a solution. For that many positions you'll hopefully be able to get circos to work, since otherwise the image would be too busy to be meaningful.